Table. Laboratory tests for commonly encountered infections .
| Syndrome and potential cause |
Culture | Non-culture methods | Notes | ||
|---|---|---|---|---|---|
| Serology | Antigen | NAAT | |||
| 1 = routine use | 2 = not routine use or unavailable | 3 = useful in special circumstances | |||
| Pharyngitis | |||||
|---|---|---|---|---|---|
| Group A streptococci | 1 | 3 | 1 | 2 | - |
| Epstein-Barr virus and cytomegalovirus | 2 | 1 | 2 | 2 | Epstein-Barr virus and cytomegalovirus NAAT is not useful in diagnosing acute pharyngitis in the immunocompetent patient. |
| Ocular infection | |||||
|---|---|---|---|---|---|
| Herpes simplex virus and adenovirus | 2 | 2 | 2 | 1 | - |
| Chlamydia trachomatis | 2 | 2 | 2 | 1 | - |
| Neisseria gonorrhoeae | 1 | 2 | 2 | 1 | Culture should be performed with NAAT where possible. |
| Other bacteria e.g. Bartonella henselae (granulomatous conjunctivitis) |
3 | 1 | 2 | 3 | - |
| Lower respiratory tract infection | |||||
|---|---|---|---|---|---|
| Respiratory viruses | 2 | 3 | 1 | 1 | Antigen testing on sputum is available for some pathogens, but is insensitive. PCR testing is preferred. |
| Mycoplasma pneumoniae | 2 | 1 | 2 | 1 | - |
| Chlamydia pneumoniae | 2 | 1 | 2 | 1 | - |
| Bordetella pertussis | 2 | 1 | 2 | 1 | - |
| Legionella species | 1 | 1 | 1 | 3 | Urinary antigen is only available for Legionella pneumophila serogroup 1. |
| Mycobacterium tuberculosis | 1 | 2 | 2 | 3 | - |
| Streptococcus pneumoniae | 1 | 2 | 1 | 3 | Pneumococcal urinary antigen is highly specific, but insensitive. It is useful as a rapid adjunct to culture. |
| Gastritis | |||||
|---|---|---|---|---|---|
| Helicobacter pylori | 3 | 1 | 1 | 2 | Culture is performed from gastric biopsies only. Diagnosis is most commonly made by urea breath test and faecal antigen. When an invasive procedure is performed endoscopy and biopsy urease testing can be used on tissue. |
| Gastroenteritis | |||||
|---|---|---|---|---|---|
| Bacteria (e.g. Salmonella) | 1 | 3 | 2 | 1 | - |
| Parasites | 2 | 3 | 1 | 1 | Serology is available for selected parasitic causes, e.g. Entamoeba histolytica |
| Viruses (e.g. noro, rota, adeno) | 2 | 2 | 1 | 1 | Antigen testing for these pathogens is relatively insensitive. NAAT (PCR) testing is preferred. |
| Toxigenic Clostridium difficile | 3 | 2 | 1 | 1 | - |
| Sexually transmitted infection | |||||
|---|---|---|---|---|---|
| Neisseria gonorrhoeae | 1 | 2 | 2 | 1 | Culture should be performed with NAAT testing where possible. |
| Chlamydia trachomatis | 2 | 2 | 2 | 1 | - |
| Mycoplasma genitalium | 2 | 2 | 2 | 1 | - |
| Trichomonas vaginalis | 2 | 2 | 2 | 1 | - |
| Syphilis | 2 | 1 | 2 | 1 | NAAT is useful for primary ulcers. Serology is the screening method of choice. |
| Systemic syndromes | |||||
|---|---|---|---|---|---|
| HIV | 2 | 1 | 1 | 3 | P24 antigen and NAAT may be useful in early seroconversion – discuss with laboratory. |
| Ross River virus and Barmah Forest virus | 2 | 1 | 2 | 2 | - |
| Rickettsia and Q fever | 2 | 1 | 2 | 3 | Some laboratories may offer NAAT. But nucleic acid is usually only detectable early in acute infection (first 7 days). |
| Leptospirosis | 3 | 1 | 2 | 3 | Leptospira can be cultured, but requires direct inoculation from blood into special media. |
| Viral exanthems | |||||
|---|---|---|---|---|---|
| Parvovirus, measles, mumps, rubella | 2 | 1 | 2 | 1 | NAAT is useful for measles (urine and blood), mumps (buccal swab) and rubella (pharyngeal swab). |
| Fever in the returned traveller | |||||
|---|---|---|---|---|---|
| Malaria | 2 | 2 | 1 | 3 | - |
| Dengue | 2 | 1 | 1 | 1 | - |
| Salmonella typhi | 1 | 3 | 2 | 2 | Culture is the mainstay of diagnosis. Serology can be of some use in retrospective diagnosis. |
NAAT nucleic acid amplification testing
PCR polymerase chain reaction